Re: [Freesurfer] error installing tensorflow

External Email - Use Caution Can you try downgrading to python 3.6 in a conda env? Python 3.7 support only TF 2.0 and higher. On Fri, 16 Apr 2021, 11:24 AJ, wrote: > External Email - Use Caution > > Hi, > > I am having trouble installing: fspython -m pip install

[Freesurfer] Running qcache on recon-all output

External Email - Use Caution Hello, I downloaded some FreeSurfer recon-all analyses from the ADNI dataset, but these analyses have been run without the qcache flag. Is there any way for me to re-analyse this with only the qcache flag? If so, how would I do this and how long would

[Freesurfer] error installing tensorflow

External Email - Use Caution Hi, I am having trouble installing: fspython -m pip install tensorflow==1.13.1 Not sure what the issue is. Any help would be greatly appreciated. best AJ Error message while installing: dyld: lazy symbol binding failed: Symbol not found: _utimensat

Re: [Freesurfer] glmfit with aseg table: view surface overlay

External Email - Use Caution Hi Doug, Thank you. Makes sense. Is there any way to visualize significance overlays for the subcortical volumes? I've also moved on to the correction for multiple comparisons in my subcortical volumes, using: mri_glmfit-sim -- glmdir

Re: [Freesurfer] Thalamic segmentation in FS voxel space

Dear George, The volumes in the text files come from soft segmentations at high resolution. There are two factors contributing to the discrepancies: 1. The downsampling to 1mm isotropic 2. The use of soft vs hard segmentations when computing volumes. For example: if you’ve got 100 voxels

Re: [Freesurfer] Failed tissue type check {Disarmed}

Hi Julie, sorry for the delay. The issue here is in finding the right segmentation for the replacement. Try --replace 29 24. The Left-undetermined voxels are actually in ventricle, so 24 replaces them with CSF. I ran it on your data, and it finished without error. On 3/8/2021 11:47 AM, Julie

Re: [Freesurfer] glmfit with aseg table: view surface overlay

The input is a table, so the output is a table (the sig.mgh file will just have the number of values that are in the table; this is not a "volume" you can look at in FV). Look in the sig.table.dat file for the sigs. On 4/13/2021 8:41 AM, Griem, Julia wrote: External Email - Use

Re: [Freesurfer] mri_segstats to report empty and non-empty segmentation

Try adding --empty On 4/12/2021 4:58 PM, miracle ozzoude wrote: External Email - Use Caution Hello Experts, I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and

Re: [Freesurfer] mkcontrast2 typo in 7.1.1

Thanks, I just fixed it and pushed the change. Should be in the next version. On 4/12/2021 3:05 PM, Ben Singer wrote: > External Email - Use Caution > > On line 106: > > if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then > > there should be a "$" before the "UseOctave" to make the line

Re: [Freesurfer] aparc+aseg to native space issue

What are the voxel sizes in the native space? It may be that if it were shifted one voxel over, it would be shifted too far in the other direction. On 4/12/2021 10:42 AM, Larson, Kathleen E wrote: External Email - Use Caution External Email - Use Caution Hi again, I

Re: [Freesurfer] Surface registration problem

This means that the source or target of the registration is not the same as what is in the registration file. Did the subject folder change? You can always delete the registration and rerun, and it will register to the new target On 4/9/2021 10:58 AM, Manenti, Giorgio wrote: >

Re: [Freesurfer] Decompressed problem during reconall

Can you send the log file of the run using the nifti as input? The file you attached is for  dicom input. On 4/8/2021 8:39 AM, Banu Femir wrote: External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7

Re: [Freesurfer] Regarding xhemi comparison of hemispheres of the same subject

Yes, I think you should be able to do that. It would be something like mris_apply_reg --sval rh.thickness --tval rh-on-lh.thickness.mgz --streg xhemi/surf/lh.fsaverage_sym surf/lh.fsaverage_sym On 4/7/2021 4:55 PM, Ghassemieh, A. (Anna) wrote: External Email - Use Caution Dear all,

Re: [Freesurfer] Skull stripping with T2

It looks like you are running a T2 through recon-all, which won't work. recon-all only takes T1-weighted. You can run it through samseg, eg, samseg --i T2_age_reg_bias.nii.gz --o samseg You can then binarize the seg.mgz to get everything inside the skull On 4/7/2021 2:17 PM, Rohan Bareja wrote:

[Freesurfer] Thalamic segmentation in FS voxel space

External Email - Use Caution Dear All, I have run segmentThalamicNuclei.sh on a set of subjects with 1mm isotropic T1 images. I need to convert these labels into volumetric space for further analysis so have been using the output with the FSvoxelSpace suffix and converting

Re: [Freesurfer] Install issue

External Email - Use Caution Thank you for the response. The computer runs Win10 pro and are under AD-control. May be there are something there out of my reach. Funny that it is almost only unpacking of some man-pages giving errors I'll try your suggestions. Pål Dr. philos.

Re: [Freesurfer] Install issue

External Email - Use Caution Hello Pal, Could be because tar archive contains hard links - which I don’t believe are supported when running a linux VM on top of a Windows OS (error from the first hard link it encountered and tried to write - and then quit). You could try

[Freesurfer] Building atlas by Xhemi: Segmentation fault (core dumped)

External Email - Use Caution Hello Freesurfer Developer， I'm building my own symmetric atlas by Xhemi, something is wrong at the final step(Make final iteration) Here is my code: make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --subjects sub_01 sub_02